Added check for valid wall_atomtype in .mdp

Otherwise, mdrun would dump core when the garbage got dereferenced.

Note that this does not need to be merged into release-4-6, because
c7a82654 already fixes it.

Fixes #700

Change-Id: I39f440595f7b112d4f01b5e32218ec45a2a97370
Merge "Added check for valid wall_atomtype in .mdp" into release-4-5-patches
Merge "Fix trjconv -sub with .trr files" into release-4-5-patches
Updating the shell completion files

Hope this g_tool -man completion technology still works!

Change-Id: I4bfd04ee1e0cc050a0690263d1e7e76f560b0372
fix OpenMP detection on Mac OS broken by a6fee0b

Compiler version check was done before the version got detected. This
code will avoid false positives even if the compiler version is not
available (although for GNUCC it should always be).

Change-Id: I554f13e4b101ae7c9f70674e966065bf9fcf2b27
remove unnecessary cmake messages

Unfortunately f8885a6 slipped in with two debug messages in the compiler
version detection code. This commit removes them so we're back to clean
& silent cmake.

Change-Id: I322183445f75688e3626e8c2382186ce1df1d0a1
Fix reading of g96 title

Change-Id: I5b077ef2f581d704848b658c588636c7510d3c38
Merge "fix OpenMP detection on Mac OS broken by a6fee0b" into release-4-6
Merge "remove unnecessary cmake messages" into release-4-6
Fixing copyright issues and code contributors

Added Mark Abraham, Christoph Junghans and
Carsten Kutzner to the list of code contributors,
per discussion with Erik and Berk.

* Now that 2013 is a copyrightable year, we need to
  assert that copyright
* No, we can't just say 1995-2013, unless we also say
  that every year in the range is a copyrightable year. I'm
  not interested in demonstrating after the fact that this is
  true for all the years before I was born. So we may as
  well start listing explicit years.
  Please read "howto (L)GPL" guides before arguing :-)
* Removed erroneous GROMACS copyright statements on
  unmodified FindBLAS.cmake,FindLAPACK.cmake,
  FindOpenMP.cmake and slightly modified FindGit.cmake
* Note Szilard's uncertainty about the origin of
  vectype_ops.cuh and thus its copyright status
* TODO for 4.6.1 deal with material in admin and scripts

References #818

Change-Id: I946200651de7f05c2ff292fcded8f33fca7b356f
thread affinity now uses some topology information

The order of logical cores on x86 is hardware and software dependent.
The cpuid topology reports this and this information is now used.
The mdrun -pinht option is generalized for SMT to -pinstride.
The mdrun -pinoffset option is now in logical (iso phyiscal) cores.
Thread-MPI no longer sets affinity, it's now all done in one place.
The option -pin is now an enum, default auto: only on when using all
cores and when no external affinity has been set.
A big NOTE is printed with auto when no pinning is used.
Option -pin on can now override thread affinity set outside mdrun.
Fixes #1122
All thread affinity code has been moved from runner.c to
gmx_thread_affinity.c.
Updated the mdrun manual for pinning also active without OpenMP.

Change-Id: Ibf0fe5882688de80c223640502c68e6170d4d044
Add colon after macro to help uncrustify

Without the colon uncrustify adds braces incorrectly

Change-Id: Ib361762c1b252de2b4a274c2be44f1fecb31b7da
Code beautification with uncrustify

We are going to try to keep our eyeballs from bleeding when we
read prehistoric code from this project while maintaining it.
So we need a point in time where release-4-6 gets beautiful
in tandem with master. That time is now.

At some point we hope to be able to do this automatically so
we can have reviewers concentrate on code quality and not
formatting trivia. But we have to do a whole-of-project
fix first.

Refs #845

Change-Id: I8e99228cc118f75c0831e8297c171fcbbabc8f73
Fix typo

Change-Id: Iba23e5cea570b2a283a19290774fe21b0e625cab
Merge release-4-5-patches into release-4-6

Conflicts:
	src/gmxlib/confio.c (whitespace only)

286575f0cd68 commit is not needed and is ignored
by this merge.

Change-Id: I7c4aabd918384aadbf6108501023ca77e019d6c1
Addendum for expanded ensemble options plus formatting fixes.

Change-Id: I4547fe74064593c939fcb292ccee056b49b292af
New major release: 4.6

* note -dev gets stripped off by the release manager by hand before
  building tarballs

Change-Id: I36fe0b8ec18c7d6f09da852e216fdf6d0a250bb7
Fix AVX double compile error

Introduced by fa181964de6c9

Note that this change will be included in the 4.6 release, therefore
this commit will effectively be the one that the 4.6 release is made
from instead of the parent.

Change-Id: Ieeede7d15109f2c44fcd2e0ef59eff2944206eab